Dive Analysis and Calibration


[Up] [Top]

Documentation for package ‘diveMove’ version 1.6.2

Help Pages

A B C D E F G L O P R S T misc

diveMove-package Dive Analysis and Calibration

-- A --

as.data.frame-method Coerce, Extractor, and Replacement methods for class "TDR" objects
as.TDRspeed Coerce, Extractor, and Replacement methods for class "TDR" objects
as.TDRspeed-method Coerce, Extractor, and Replacement methods for class "TDR" objects
austFilter Filter satellite locations

-- B --

bec Calculate bout ending criteria from model coefficients
bec-method Calculate bout ending criteria from model coefficients
boutfreqs Histogram of log-transformed frequencies
boutinit Fit "broken stick" model to log frequency data for identification of bouts of behaviour
boutinit-method Fit "broken stick" model to log frequency data for identification of bouts of behaviour
Bouts Class "Bouts" for representing Poisson mixtures for identification of behavioural bouts
Bouts-class Class "Bouts" for representing Poisson mixtures for identification of behavioural bouts
boutsCDF Estimated cumulative frequency for two- or three-process Poisson mixture models
boutsNLSll Generalized log likelihood function taking any number of Poisson processes in a "broken-stick" model
boutsNLSll-method Generalized log likelihood function taking any number of Poisson processes in a "broken-stick" model

-- C --

calibrateDepth Calibrate Depth and Generate a "TDRcalibrate" object
calibrateSpeed Calibrate and build a "TDRcalibrate" object
ccData<- Coerce, Extractor, and Replacement methods for class "TDR" objects
ccData<--method Coerce, Extractor, and Replacement methods for class "TDR" objects
coerce-method Coerce, Extractor, and Replacement methods for class "TDR" objects
createTDR Read comma-delimited file with "TDR" data

-- D --

depth<- Coerce, Extractor, and Replacement methods for class "TDR" objects
depth<--method Coerce, Extractor, and Replacement methods for class "TDR" objects
distSpeed Calculate distance and speed between locations
diveModel Class "diveModel" for representing a model for identifying dive phases
diveModel-class Class "diveModel" for representing a model for identifying dive phases
diveMove Dive Analysis and Calibration
dives Sample of TDR data from a fur seal
diveStats Per-dive statistics
divesTDR Sample of TDR data from a fur seal
divesTDRzoc Sample of TDR data from a fur seal

-- E --

extractDive Extract Dives from "TDR" or "TDRcalibrate" Objects
extractDive-method Extract Dives from "TDR" or "TDRcalibrate" Objects

-- F --

fitMLEbouts Maximum Likelihood Model of mixtures of 2 or 3 Poisson Processes
fitMLEbouts-method Maximum Likelihood Model of mixtures of 2 or 3 Poisson Processes
fitNLSbouts Fit mixture of Poisson Processes to Log Frequency data via Non-linear Least Squares regression
fitNLSbouts-method Fit mixture of Poisson Processes to Log Frequency data via Non-linear Least Squares regression

-- G --

getCCData Coerce, Extractor, and Replacement methods for class "TDR" objects
getCCData-method Coerce, Extractor, and Replacement methods for class "TDR" objects
getDAct Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDAct-method Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDepth Coerce, Extractor, and Replacement methods for class "TDR" objects
getDepth-method Coerce, Extractor, and Replacement methods for class "TDR" objects
getDiveDeriv Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDiveDeriv-method Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDiveModel Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDiveModel-method Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDPhaseLab Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDPhaseLab-method Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getDtime Coerce, Extractor, and Replacement methods for class "TDR" objects
getDtime-method Coerce, Extractor, and Replacement methods for class "TDR" objects
getFileName Coerce, Extractor, and Replacement methods for class "TDR" objects
getFileName-method Coerce, Extractor, and Replacement methods for class "TDR" objects
getGAct Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getGAct-method Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getSpeed Coerce, Extractor, and Replacement methods for class "TDR" objects
getSpeed-method Coerce, Extractor, and Replacement methods for class "TDR" objects
getSpeedCoef Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getSpeedCoef-method Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getTDR Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getTDR-method Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
getTime Coerce, Extractor, and Replacement methods for class "TDR" objects
getTime-method Coerce, Extractor, and Replacement methods for class "TDR" objects
grpSpeedFilter Filter satellite locations

-- L --

labelBouts Label each vector element or matrix row with bout membership number
labelBouts-method Label each vector element or matrix row with bout membership number

-- O --

oneDiveStats Per-dive statistics

-- P --

plotBouts Plot fitted Poisson mixture model and data
plotBouts-method Plot fitted Poisson mixture model and data
plotBoutsCDF Plot empirical and deterministic cumulative frequency distribution Poisson mixture data and model
plotBoutsCDF-method Plot empirical and deterministic cumulative frequency distribution Poisson mixture data and model
plotDiveModel Methods for plotting models of dive phases
plotDiveModel-method Methods for plotting models of dive phases
plotTDR Methods for plotting objects of class "TDR" and "TDRcalibrate"
plotTDR-method Methods for plotting objects of class "TDR" and "TDRcalibrate"
plotZOC Methods for visually assessing results of ZOC procedure
plotZOC-method Methods for visually assessing results of ZOC procedure

-- R --

readLocs Read comma-delimited file with location data
readTDR Read comma-delimited file with "TDR" data
rmixexp Generate samples from a mixture of exponential distributions
rmsDistFilter Filter satellite locations
rqPlot Plot of quantile regression for speed calibrations

-- S --

sealLocs Ringed and Gray Seal ARGOS Satellite Location Data
show-method Coerce, Extractor, and Replacement methods for class "TDR" objects
show-method Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
speed<- Coerce, Extractor, and Replacement methods for class "TDR" objects
speed<--method Coerce, Extractor, and Replacement methods for class "TDR" objects
stampDive Per-dive statistics

-- T --

TDR Classes "TDR" and "TDRspeed" for representing TDR information
TDR-accessors Coerce, Extractor, and Replacement methods for class "TDR" objects
TDR-class Classes "TDR" and "TDRspeed" for representing TDR information
TDR-methods Coerce, Extractor, and Replacement methods for class "TDR" objects
TDRcalibrate Class "TDRcalibrate" for dive analysis
TDRcalibrate-accessors Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
TDRcalibrate-class Class "TDRcalibrate" for dive analysis
TDRcalibrate-methods Methods to Show and Extract Basic Information from "TDRcalibrate" Objects
TDRspeed Classes "TDR" and "TDRspeed" for representing TDR information
TDRspeed-class Classes "TDR" and "TDRspeed" for representing TDR information
timeBudget Describe the Time Budget of Major Activities from "TDRcalibrate" object.
timeBudget-method Describe the Time Budget of Major Activities from "TDRcalibrate" object.

-- misc --

.runquantile Quantile of Moving Window
[-method Coerce, Extractor, and Replacement methods for class "TDR" objects